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Geographic Transmission and Epidemic History of HIV-1 CRF01_AE, CRF07_BC, and HCV Subtype-6w among Taiwanese Persons Who Inject Drugs. Viruses 2022; 14:v14102142. [PMID: 36298695 PMCID: PMC9610456 DOI: 10.3390/v14102142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/19/2022] [Accepted: 09/25/2022] [Indexed: 11/30/2022] Open
Abstract
Persons who inject drugs (PWID) and their risk-related behaviors (e.g., unprotected sex and sharing needles/syringes/other injection equipment) have caused severe public health problems, especially in the rapid spread of HIV-1 and HCV. Here, we reconstructed the epidemic history of HIV-1 circulating recombinant form (CRF) 01_AE, CRF07_BC, and HCV subtype-6w among Taiwanese PWID. The timescales were estimated using phylogenetic and Bayesian coalescent analyses. The results revealed that CRF01_AE started to circulate in the Taiwanese PWID population in central Taiwan at 1992.5 (95% credible region: 1988.8–1995.9) and spread to other regions of Taiwan, while CRF07_BC was first identified in southern Taiwan at 2000.0 (95% CR: 1997.8–2002.2) and then spread northward to central-northern Taiwan. All HCV-6 strains were from Asia (that is, China, Myanmar, Taiwan, and Vietnam) and originated in 1928.1 (95% CR: 1890.2–1966.0). Furthermore, subtype-6w isolates from different regions of Taiwan appeared to share a common source that existed in the mid-1990s (95% CR: 1985.0–2001.8) or thereabouts. The routes of drug trafficking and the resulting high prevalence of HIV-1/HCV co-infections among PWID might have contributed to the virus transmission and promoted its spread worldwide. Long-term monitoring and policy implementation in at-risk populations would be useful for disease control.
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Zhou Y, Huang S, Cui M, Guo Z, Tang H, Lyu H, Ni Y, Lu Y, Feng Y, Wang Y, Jing F, Huang S, Li J, Xu Y, Mei W. Comparison between HIV self-testing and facility-based HIV testing approach on HIV early detection among men who have sex with men: A cross-sectional study. Front Immunol 2022; 13:857905. [PMID: 36177052 PMCID: PMC9513029 DOI: 10.3389/fimmu.2022.857905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022] Open
Abstract
Background To assess whether HIV self-testing (HIVST) has a better performance in identifying HIV-infected cases than the facility-based HIV testing (HIVFBT) approach. Methods A cross-sectional study was conducted among men who have sex with men (MSM) by using an online questionnaire (including information on sociodemographic, sexual biography, and HIV testing history) and blood samples (for limiting antigen avidity enzyme immunoassay, gene subtype testing, and taking confirmed HIV test). MSM who were firstly identified as HIV positive through HIVST and HIVFBT were compared. Chi-square or Fisher’s exact test was used to explore any association between both groups and their subgroups. Results In total, 124 MSM HIV cases were identified from 2017 to 2021 in Zhuhai, China, including 60 identified through HIVST and 64 through HIVFBT. Participants in the HIVST group were younger (≤30 years, 76.7% vs. 46.9%), were better educated (>high school, 61.7% vs. 39.1%), and had higher viral load (≥1,000 copies/ml, 71.7% vs. 50.0%) than MSM cases identified through HIVFBT. The proportion of early HIV infection in the HIVST group was higher than in the HIVFBT group, identified using four recent infection testing algorithms (RITAs) (RITA 1, 46.7% vs. 25.0%; RITA 2, 43.3% vs. 20.3%; RITA 3, 30.0% vs. 14.1%; RITA 4, 26.7% vs. 10.9%; all p < 0.05). Conclusions The study showed that HIVST has better HIV early detection among MSM and that recent HIV infection cases mainly occur in younger and better-educated MSM. Compared with HIVFBT, HIVST is more accessible to the most at-risk population on time and tends to identify the case early. Further implementation studies are needed to fill the knowledge gap on this medical service model among MSM and other target populations.
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Affiliation(s)
- Yi Zhou
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai, China
- Faculty of Medicine, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Shaoli Huang
- Zhejiang University-University of Edinburgh Institute, Zhejiang University-University, Hangzhou, China
| | - Mingting Cui
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Zhihui Guo
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Haotong Tang
- Faculty of Medicine, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Hang Lyu
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Yuxin Ni
- Dermatology Hospital of South Medical University, Guangzhou, China
- University of North Carolina Project-China, Guangzhou, China
| | - Ying Lu
- Dermatology Hospital of South Medical University, Guangzhou, China
- University of North Carolina Project-China, Guangzhou, China
| | - Yunlong Feng
- Department of Public Health and Preventive Medicine, School of Medicine Jinan University, Guangzhou, China
| | - Yuyu Wang
- Department of Public Health and Preventive Medicine, School of Medicine Jinan University, Guangzhou, China
| | - Fengshi Jing
- Institute for Healthcare Artificial Intelligence, Guangdong Second Provincial General Hospital, Guangzhou, China
- School of Data Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Shanzi Huang
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Jiarun Li
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai, China
| | - Yao Xu
- Department of Paediatrics, School of Clinical Science, Monash University, Melbourne, VIC, Australia
- *Correspondence: Wenhua Mei, ; Yao Xu,
| | - Wenhua Mei
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai, China
- *Correspondence: Wenhua Mei, ; Yao Xu,
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Jiang H, Lan G, Zhu Q, Feng Y, Liang S, Li J, Zhou X, Lin M, Shao Y. Impacts of HIV-1 Subtype Diversity on Long-Term Clinical Outcomes in Antiretroviral Therapy in Guangxi, China. J Acquir Immune Defic Syndr 2022; 89:583-591. [PMID: 34966146 PMCID: PMC8900993 DOI: 10.1097/qai.0000000000002906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Comprehensively estimating the impacts of HIV-1 subtype diversity on long-term clinical outcomes during antiretroviral therapy (ART) can help inform program recommendations. METHODS The HIV-1 sequence data and clinical records of 5950 patients from all 14 prefectures in Guangxi, China, during 2008-2020 were included. Evolutional trends of CD4+ T-lymphocyte count and viral load were explored, and the effects of HIV-1 subtypes on clinical outcomes were estimated by the Cox proportional hazards model. The polymorphisms involved in drug resistance mutation were analyzed. RESULTS Compared with patients with CRF07_BC, patients with CRF01_AE and CRF08_BC showed poor immunologic and virologic responses to antiretroviral therapy. Although the median expected time from ART initiation to virologic suppression for all patients was approximately 12 months, patients with CRF01_AE and CRF08_BC had a long time to achieve immune recovery and a short time to occur immunologic failure, compared with patients with CRF07_BC. Adjusted analysis showed that both CRF01_AE and CRF08_BC were the negative factors in immune recovery and long-term mortality. In addition, CRF08_BC was a negative factor in virologic suppression and a risk factor of virologic failure. This poor virologic response might result from the high prevalence of drug resistance mutation in CRF08_BC. CONCLUSIONS Compared with patients with CRF07_BC, patients with CRF01_AE could benefit more from immediate ART, and patients with CRF08_BC are more suitable for PI-based regimens. These data emphasize the importance of routine HIV-1 genotyping before ART, immediate ART, and personalized ART regimens to improve the prognosis for patients undergoing ART.
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Affiliation(s)
- He Jiang
- Guangxi Key Laboratory of AIDS Prevention and Control and Achievement Transformation, Guangxi Center for Disease Prevention and Control, Nanning, Guangxi, China
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China; and
- State of Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, China
| | - Guanghua Lan
- Guangxi Key Laboratory of AIDS Prevention and Control and Achievement Transformation, Guangxi Center for Disease Prevention and Control, Nanning, Guangxi, China
| | - Qiuying Zhu
- Guangxi Key Laboratory of AIDS Prevention and Control and Achievement Transformation, Guangxi Center for Disease Prevention and Control, Nanning, Guangxi, China
| | - Yi Feng
- State of Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, China
| | - Shujia Liang
- Guangxi Key Laboratory of AIDS Prevention and Control and Achievement Transformation, Guangxi Center for Disease Prevention and Control, Nanning, Guangxi, China
| | - Jianjun Li
- Guangxi Key Laboratory of AIDS Prevention and Control and Achievement Transformation, Guangxi Center for Disease Prevention and Control, Nanning, Guangxi, China
| | - Xinjuan Zhou
- Guangxi Key Laboratory of AIDS Prevention and Control and Achievement Transformation, Guangxi Center for Disease Prevention and Control, Nanning, Guangxi, China
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China; and
| | - Mei Lin
- Guangxi Key Laboratory of AIDS Prevention and Control and Achievement Transformation, Guangxi Center for Disease Prevention and Control, Nanning, Guangxi, China
| | - Yiming Shao
- Guangxi Key Laboratory of AIDS Prevention and Control and Achievement Transformation, Guangxi Center for Disease Prevention and Control, Nanning, Guangxi, China
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China; and
- State of Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, China
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CRF07_BC is associated with slow HIV disease progression in Chinese patients. Sci Rep 2022; 12:3773. [PMID: 35260599 PMCID: PMC8904811 DOI: 10.1038/s41598-022-07518-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
HIV subtypes convey important epidemiological information and possibly influence the rate of disease progression. In this study, HIV disease progression in patients infected with CRF01_AE, CRF07_BC, and subtype B was compared in the largest HIV molecular epidemiology study ever done in China. A national data set of HIV pol sequences was assembled by pooling sequences from public databases and the Beijing HIV laboratory network. Logistic regression was used to assess factors associated with the risk of AIDS at diagnosis ([AIDSAD], defined as a CD4 count < 200 cells/µL) in patients with HIV subtype B, CRF01_AE, and CRF07_BC. Of the 20,663 sequences, 9,156 (44.3%) were CRF01_AE. CRF07_BC was responsible for 28.3% of infections, followed by B (13.9%). In multivariable analysis, the risk of AIDSAD differed significantly according to HIV subtype (OR for CRF07_BC vs. B: 0.46, 95% CI 0.39─0.53), age (OR for ≥ 65 years vs. < 18 years: 4.3 95% CI 1.81─11.8), and transmission risk groups (OR for men who have sex with men vs. heterosexuals: 0.67 95% CI 0.6─0.75). These findings suggest that HIV diversity in China is constantly evolving and gaining in complexity. CRF07_BC is less pathogenic than subtype B, while CRF01_AE is as pathogenic as B.
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Cho YK, Kim JE, Lee J. Impact of HIV-1 subtypes on gross deletion in the nef gene after Korean Red Ginseng treatment. J Ginseng Res 2022; 46:731-737. [PMID: 36312730 PMCID: PMC9597433 DOI: 10.1016/j.jgr.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022] Open
Abstract
Background Methods Results Conclusion
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Ekenberg C, Reekie J, Zucco AG, Murray DD, Sharma S, Macpherson CR, Babiker A, Kan V, Lane HC, Neaton JD, Lundgren JD. The association of human leukocyte antigen alleles with clinical disease progression in HIV-positive cohorts with varied treatment strategies. AIDS 2021; 35:783-789. [PMID: 33587436 PMCID: PMC7969421 DOI: 10.1097/qad.0000000000002800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The Strategic Timing of AntiRetroviral Treatment (START) and Strategies for Management of Antiretroviral Therapy (SMART) trials demonstrated that ART can partly reverse clinically defined immune dysfunction induced by HIV replication. As control of HIV replication is influenced by the HLA region, we explored whether HLA alleles independently influence the risk of clinical events in HIV+ individuals. DESIGN Cohort study. METHODS In START and SMART participants, associations between imputed HLA alleles and AIDS, infection-related cancer, herpes virus-related AIDS events, chronic inflammation-related conditions, and bacterial pneumonia were assessed. Cox regression was used to estimate hazard ratios for the risk of events among allele carriers versus noncarriers. Models were adjusted for sex, age, geography, race, time-updated CD4+ T-cell counts and HIV viral load and stratified by treatment group within trials. HLA class I and II alleles were analyzed separately. The Benjamini--Hochberg procedure was used to limit the false discovery rate to less than 5% (i.e. q value <0.05). RESULTS Among 4829 participants, there were 132 AIDS events, 136 chronic inflammation-related conditions, 167 bacterial pneumonias, 45 infection-related cancers, and 49 herpes virus-related AIDS events. Several associations with q value less than 0.05 were found: HLA-DQB1∗06:04 and HLA-DRB1∗13:02 with AIDS (adjusted HR [95% CI] 2.63 [1.5-4.6] and 2.25 [1.4-3.7], respectively), HLA-B∗15:17 and HLA-DPB1∗15:01 with bacterial pneumonia (4.93 [2.3-10.7] and 4.33 [2.0-9.3], respectively), and HLA-A∗69:01 with infection-related cancer (15.26 [3.5-66.7]). The carriage frequencies of these alleles were 10% or less. CONCLUSION This hypothesis-generating study suggests that certain HLA alleles may influence the risk of immune dysfunction-related events irrespective of viral load and CD4+ T-cell count.
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Affiliation(s)
- Christina Ekenberg
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Joanne Reekie
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Adrian G Zucco
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Daniel D Murray
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Shweta Sharma
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Cameron R Macpherson
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Abdel Babiker
- Medical Research Council, Clinical Trials Unit in University College London, London, United Kingdom
| | - Virginia Kan
- Veterans Affairs Medical Center and George Washington University, Washington DC
| | - H Clifford Lane
- National Institute of Allergy and Infectious Diseases, Division of Clinical Research, Bethesda, Maryland, USA
| | - James D Neaton
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jens D Lundgren
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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Aulicino PC, Zapiola I, Kademian S, Valle MM, Fernandez Giuliano S, Toro R, Barbas G, Cañizal AM, Mayon P, Golemba MD, Ortiz de Zarate M, Corazza MS, Cudola A, Mecikovsky D, Bologna R, Mangano A, Sen L. Pre-treatment drug resistance and HIV-1 subtypes in infants from Argentina with and without exposure to antiretroviral drugs for prevention of mother-to-child transmission. J Antimicrob Chemother 2020; 74:722-730. [PMID: 30517632 DOI: 10.1093/jac/dky486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES To assess the prevalence and patterns of pre-treatment HIV drug resistance (PDR) and HIV-1 subtype in infants from Argentina with exposure to different antiretroviral drugs (ARVs) for the prevention of mother-to-child transmission (PMTCT). PATIENTS AND METHODS HIV-1 genotyping was performed in 115 infants (median age = 2.3 months) born between 2007 and 2014 to screen for drug resistance mutations (DRMs) before starting first-line ART. HIV-1 subtype was characterized by phylogenetic and recombination analysis. RESULTS Overall, DRMs were found in 34 of 115 infants (PDR level 30% to any ARV, 3.5% to PIs, 12% to NRTIs and 22% to NNRTIs). Of the 115 infants, 22 (19.1%) were ARV-unexposed. Another 93 were ARV-exposed: 28 (24.3%) to short-course zidovudine monotherapy ARV prophylaxis; 25 (21.7%) to nevirapine-based ARV prophylaxis; 12 (10.4%) to perinatal infant zidovudine prophylaxis + maternal combination ART with NNRTIs; and 28 (24.3%) to perinatal infant zidovudine prophylaxis+maternal combination ART with PIs. Transmitted drug resistance among ARV-unexposed infants was 32% (5% to PIs, 9% to NRTIs and 18% to NNRTIs). ART-exposed infants showed multi-class ARV resistance. Importantly, vertical transmission of a triple-class-resistant virus was confirmed in one case. Patterns of DRMs predicted high-level resistance to NNRTIs in a similar and high proportion (>50%) of infants with at least one DRM independently of ARV exposure. BF recombinants were found in 74%, subtype B in 20%, subtype C in 3% and novel AG and AB recombinants in 3%. CONCLUSIONS PDR in HIV-1-infected children from Argentina is among the highest reported, jeopardizing successful lifelong suppressive ART as well as the efficacy of current PMTCT regimens.
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Affiliation(s)
- Paula C Aulicino
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
| | - Ines Zapiola
- Unidad de Virología, Hospital de Infecciosas "Francisco J. Muñiz", Buenos Aires, Argentina
| | - Silvia Kademian
- Laboratorio Central, Ministerio de Salud, Córdoba, Argentina
| | - María M Valle
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | | | - Rosana Toro
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Gabriela Barbas
- Laboratorio Central, Ministerio de Salud, Córdoba, Argentina
| | - Ana M Cañizal
- Unidad de Virología, Hospital de Infecciosas "Francisco J. Muñiz", Buenos Aires, Argentina
| | - Paula Mayon
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Marcelo D Golemba
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
| | | | - Marisa S Corazza
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Analía Cudola
- Laboratorio Central, Ministerio de Salud, Córdoba, Argentina
| | - Débora Mecikovsky
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Rosa Bologna
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
| | - Luisa Sen
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
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The Examination of Viral Characteristics of HIV-1 CRF07_BC and Its Potential Interaction with Extracellular Galectin-3. Pathogens 2020; 9:pathogens9060425. [PMID: 32485969 PMCID: PMC7350312 DOI: 10.3390/pathogens9060425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 11/16/2022] Open
Abstract
HIV-1 CRF07_BC is a B’ and C subtype recombinant emerging virus and many of its viral characteristics remain unclear. Galectin-3 (Gal3) is a β-galactose binding lectin that has been reported as a pattern recognition receptor (PRR) and is known to mediate adhesion between cells and microbes. This study aims to examine the viral characteristics of HIV-1 CRF07_BC virus and the role of extracellular galectin-3 in HIV-1 CRF07_BC infection. A total of 28 HIV-1+ injecting drug users (IDUs) were recruited and 24 (85.7%) were identified as HIV-1 CRF07_BC. Results indicate that significant higher serum galectin-3 was measured in CRF07_BC infected patients and CRF07_BC infection triggered significant galectin-3 expression (p < 0.01). Viral characteristics demonstrate that CRF07_BC virions display a higher level of envelope gp120 spikes. The virus infectivity assay demonstrated that co-treatment with galectin-3 significantly promoted CRF07_BC attachment and internalization (p < 0.01). A co-immunoprecipitation assay showed that pulldown galectin-3 co-precipitated both CD4 and gp120 proteins. Results from an enzyme-linked immunosorbent assay (ELISA) indicate that the galectin-3 promoting effect occurs through enhancement of the interaction between gp120 and CD4. This study suggests that CRF07_BC was predominant in HIV-1+ IDUs and CRF07_BC utilized extracellular galectin-3 to enhance its infectivity via stabilization of the gp120-CD4 interaction.
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Ekenberg C, Tang MH, Zucco AG, Murray DD, MacPherson CR, Hu X, Sherman BT, Losso MH, Wood R, Paredes R, Molina JM, Helleberg M, Jina N, Kityo CM, Florence E, Polizzotto MN, Neaton JD, Lane HC, Lundgren JD. Association Between Single-Nucleotide Polymorphisms in HLA Alleles and Human Immunodeficiency Virus Type 1 Viral Load in Demographically Diverse, Antiretroviral Therapy-Naive Participants From the Strategic Timing of AntiRetroviral Treatment Trial. J Infect Dis 2020; 220:1325-1334. [PMID: 31219150 DOI: 10.1093/infdis/jiz294] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/05/2019] [Indexed: 12/18/2022] Open
Abstract
The impact of variation in host genetics on replication of human immunodeficiency virus type 1 (HIV-1) in demographically diverse populations remains uncertain. In the current study, we performed a genome-wide screen for associations of single-nucleotide polymorphisms (SNPs) to viral load (VL) in antiretroviral therapy-naive participants (n = 2440) with varying demographics from the Strategic Timing of AntiRetroviral Treatment (START) trial. Associations were assessed using genotypic data generated by a customized SNP array, imputed HLA alleles, and multiple linear regression. Genome-wide significant associations between SNPs and VL were observed in the major histocompatibility complex class I region (MHC I), with effect sizes ranging between 0.14 and 0.39 log10 VL (copies/mL). Supporting the SNP findings, we identified several HLA alleles significantly associated with VL, extending prior observations that the (MHC I) is a major host determinant of HIV-1 control with shared genetic variants across diverse populations and underscoring the limitations of genome-wide association studies as being merely a screening tool.
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Affiliation(s)
- Christina Ekenberg
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Man-Hung Tang
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Adrian G Zucco
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Daniel D Murray
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Cameron Ross MacPherson
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Xiaojun Hu
- Laboratory of Human Retrovirology and Immunoinformatics, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Bethesda, Maryland
| | - Brad T Sherman
- Laboratory of Human Retrovirology and Immunoinformatics, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Bethesda, Maryland
| | - Marcelo H Losso
- Hospital General de Agudos JM Ramos, Buenos Aires, Argentina
| | - Robin Wood
- Desmond Tutu HIV Foundation Clinical Trials Unit, Cape Town, South Africa
| | - Roger Paredes
- Infectious Diseases Service and irsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Jean-Michel Molina
- Department of Infectious Diseases, University of Paris Diderot, Sorbonne Paris Cité, and Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, France
| | - Marie Helleberg
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Nureen Jina
- Clinical HIV Research Unit, Wits Health Consortium, Department of Medicine, University of the Witwatersrand, Helen Joseph Hospital, Themba Lethu Clinic, Johannesburg, South Africa
| | | | | | | | - James D Neaton
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis
| | - H Clifford Lane
- National Institute of Allergy and Infectious Diseases, Division of Clinical Research, Bethesda, Maryland
| | - Jens D Lundgren
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
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Chaplin B, Akanmu AS, Inzaule SC, Samuels JO, Okonkwo P, Ilesanmi O, Adewole IFA, Asadu C, Khamofu H, Mpazanje R, Ndembi N, Odafe S, Sigaloff KCE, Ngige EN, Abatta EO, Akinbiyi G, Dakum P, Rinke de Wit TF, Kanki P. Association between HIV-1 subtype and drug resistance in Nigerian infants. J Antimicrob Chemother 2020; 74:172-176. [PMID: 30260417 DOI: 10.1093/jac/dky380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/24/2018] [Indexed: 11/13/2022] Open
Abstract
Background Many lines of evidence point to HIV-1 subtype-specific differences in the development of drug resistance mutations. While variation between subtype C and others has been extensively explored, there has been less emphasis on subtypes common to West Africa. We examined a previously described national survey of pretreatment drug resistance in HIV-1-infected Nigerian children aged <18 months, to explore the association between subtypes and patterns of resistance. Methods Five hundred and forty-nine dried blood spots, from 15 early infant diagnostic facilities in Nigeria, were amplified and HIV-1 polymerase was sequenced. Four hundred and twenty-four were analysed for surveillance drug resistance mutations (SDRMs). Associations between subtype and SDRMs were evaluated by Fisher's exact test and logistic regression analysis, controlling for geographical region and exposure. Results Using the sub-subtypes of HIV-1 G defined by Delatorre et al. (PLoS One 2014. 9 e98908) the most common subtypes were CRF02_AG (174, 41.0%), GWA-I (128, 30.2%), GWA-II (24, 5.7%), GCA (11, 2.6%), A (21, 5.0%) and CRF06_cpx (18, 4.2%). One hundred and ninety infants (44.8%) had ≥1 NNRTI mutation, 92 infants (21.7%) had ≥1 NRTI mutation and 6 infants (1.4%) had ≥1 PI mutation. By logistic regression, 67N was more common in GWA-II/GCA than CRF02_AG (OR 12.0, P = 0.006), as was 70R (OR 23.1, P = 0.007), 184I/V (OR 2.92, P = 0.020), the presence of ≥1 thymidine analogue mutation (TAM) (OR 3.87, P = 0.014), ≥1 type 2 TAM (OR 7.61, P = 0.001) and ≥1 NRTI mutation (OR 3.26, P = 0.005). Conclusions This dataset reveals differences among SDRMs by subtype; in particular, between the GWA-II and GCA subclades, compared with CRF02_AG and GWA-I.
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Affiliation(s)
- Beth Chaplin
- Department of Immunology & Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Alani Sulaimon Akanmu
- Department of Haematology and Blood Transfusion, College of Medicine of the University of Lagos, Lagos, Nigeria
| | - Seth C Inzaule
- Amsterdam Institute for Global Health and Development & Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Isaac F A Adewole
- Department of Obstetrics and Gynaecology, University of Ibadan, and the Federal Ministry of Health, Abuja, Nigeria
| | | | | | | | | | - Solomon Odafe
- Centers for Disease Control and Prevention, Abuja, Nigeria
| | - Kim C E Sigaloff
- Amsterdam Institute for Global Health and Development & Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Patrick Dakum
- Institute of Human Virology in Nigeria, Abuja, Nigeria
| | - Tobias F Rinke de Wit
- Amsterdam Institute for Global Health and Development & Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Phyllis Kanki
- Department of Immunology & Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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11
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Liang Y, Han Z, Shui J, Cheng W, Zhong F, Cai Q, Wang H, Wu H, Xu H, Tang S. HIV-1 genotype is independently associated with immunodeficiency progression among Chinese men who have sex with men: an observational cohort study. HIV Med 2019; 21:279-288. [PMID: 31863622 DOI: 10.1111/hiv.12823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVES HIV-1 genetic diversity is increasing among men who have sex with men (MSM) in China, but the association of HIV-1 genotype with disease progression remains to be elucidated. METHODS We collected data in an observational longitudinal cohort study of 860 HIV-1-infected MSM in Guangzhou, China between January 2008 and March 2017. Kaplan-Meier analysis and Cox proportional hazard model were used to predict the time from HIV-1 diagnosis to immunodeficiency progression (CD4 cell count < 200 cells/μl) as well as adjusted hazard ratio (aHR). RESULTS CRF01_AE and HIV-1 subtype B infection were associated with higher percentage of patients progressed to immunodeficiency and higher incidence of immunodeficiency than infection with CRF07_BC or CRF55_01B. Compared with CRF07_BC, the time from HIV-1 diagnosis to immunodeficiency were different among the major HIV-1 genotypes, which ranked as follows, in descending order: CRF07_BC (7.03 years) > CRF55_01B (5.71 years, P = 0.014; aHR 3.752, P = 0.0923) > CRF01_AE (5.18 years, P < 0.001; aHR 4.733, P = 0.0152). HIV-1 genotype, viral load and baseline CD4 T-cell count were three independent variables associated with disease progression. CONCLUSIONS Our results confirm differential rates of immunodeficiency progression as a function of HIV-1 genotype. The impact of HIV-1 genotype on HIV epidemics, patient management and prevention should be further investigated.
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Affiliation(s)
- Y Liang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou, China
| | - Z Han
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - J Shui
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou, China
| | - W Cheng
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - F Zhong
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Q Cai
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou, China
| | - H Wang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou, China
| | - H Wu
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - H Xu
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - S Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Dermatology Hospital, Southern Medical University, Guangzhou, China
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12
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High polymorphism rates in well-known T cell epitopes restricted by protective HLA alleles during HIV infection are associated with rapid disease progression in early-infected MSM in China. Med Microbiol Immunol 2019; 208:239-251. [PMID: 30848362 DOI: 10.1007/s00430-019-00585-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/21/2019] [Indexed: 11/26/2022]
Abstract
T cell epitopes restricted by several protective HLA alleles, such as B*57, B*5801, B*27, B*51 and B*13, have been very well defined over the past two decades. We investigated 32 well-known T cell epitopes restricted by protective HLA molecules among 54 Chinese men who have sex with men (MSM) at the early stage of HIV-1 infection. Subjects in our cohort carrying protective HLA types did not exhibit slow CD4 T cell count decline (P = 0.489) or low viral load set points (P = 0.500). Variations occurred in 96.88% (31/32) of the known wild-type epitopes (rate 1.85-100%), and the variation rates of the strains of two CRF01_AE lineages were significantly higher than those of non-CRF01_AE strains (76.82% vs. 48.96%, P = 0.004; 71.27% vs. 8.96%, P = 0.025). Subjects infected with CRF01_AE exhibited relatively rapid disease progression (P = 0.035). Therefore, the lack of wild-type protective T cell epitopes restricted by classic protective HLA alleles in CRF01_AE HIV-1 strains may be one of the reasons why rapid disease progression is observed in Chinese MSM with HIV-1 infection.
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13
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Tough RH, McLaren PJ. Interaction of the Host and Viral Genome and Their Influence on HIV Disease. Front Genet 2019; 9:720. [PMID: 30728828 PMCID: PMC6351501 DOI: 10.3389/fgene.2018.00720] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/21/2018] [Indexed: 01/23/2023] Open
Abstract
The course of Human Immunodeficiency Virus type 1 (HIV) infection is a dynamic interplay in which both host and viral genetic variation, among other factors, influence disease susceptibility and rate of progression. HIV set-point viral load (spVL), a key indicator of HIV disease progression, has an estimated 30% of variance attributable to common heritable effects and roughly 70% attributable to environmental factors and/or additional non-genetic factors. Genome-wide genotyping and sequencing studies have allowed for large-scale association testing studying host and viral genetic variants associated with infection and disease progression. Host genomics of HIV infection has been studied predominantly in Caucasian populations consistently identifying human leukocyte antigen (HLA) genes and C-C motif chemokine receptor 5 as key factors of HIV susceptibility and progression. However, these studies don’t fully assess all classes of genetic variation (e.g., very rare polymorphisms, copy number variants etc.) and do not inform on non-European ancestry groups. Additionally, viral sequence variability has been demonstrated to influence disease progression independently of host genetic variation. Viral sequence variation can be attributed to the rapid evolution of the virus within the host due to the selective pressure of the host immune response. As the host immune system responds to the virus, e.g., through recognition of HIV antigens, the virus is able to mitigate this response by evolving HLA-specific escape mutations. Diversity of viral genotypes has also been correlated with moderate to strong effects on CD4+ T cell decline and some studies showing weak to no correlation with spVL. There is evidence to support these viral genetic factors being heritable between individuals and the evolution of these factors having important consequences in the genetic epidemiology of HIV infection on a population level. This review will discuss the host-pathogen interaction of HIV infection, explore the importance of host and viral genetics for a better understanding of pathogenesis and identify opportunities for additional genetic studies.
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Affiliation(s)
- Riley H Tough
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
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14
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Bobkova MR. [Genetic diversity of human immunodeficiency viruses and antiretroviral therapy]. TERAPEVT ARKH 2018; 88:103-111. [PMID: 28005040 DOI: 10.17116/terarkh20168811103-111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The lecture is devoted to the analysis of the state-of-the-art of the impact of genetic diversity of human immunodeficiency (HIV) viruses on the pattern of infection and the efficiency of antiretroviral therapy (ART). It provides brief information on the origin and evolution of HIV and on the current classification of their genetic variants. The molecular epidemiological situation of HIV infection in Russia and nearby states and the major molecular HIV variants that are dominant in these countries, as well as their origin and prevalence trends are characterized. How the diversity of HIV can affect the efficiency of diagnosis, the transmission of the virus, and the pattern of HIV pathogenesis are briefly reviewed. The comparative data available in the world's scientific literature on these topics are given. More detailed attention is given to the possible causes of varying therapeutic effects against different HIV subtypes, as well as to the specific features of the formation and phenotyping manifestation of ART drug resistance mutations. There is evidence for the necessity of forming a unified follow-up system for treated HIV-infected patients during ART scaling, including in an effort to evaluate the impact of the specific features of the HIV genome on the efficiency of treatment regimens used in Russia.
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Affiliation(s)
- M R Bobkova
- D.I. Ivanovsky Institute of Virology, Honorary Acad. N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
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15
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Abstract
The evolution of viral pathogens is shaped by strong selective forces that are exerted during jumps to new hosts, confrontations with host immune responses and antiviral drugs, and numerous other processes. However, while undeniably strong and frequent, adaptive evolution is largely confined to small parts of information-packed viral genomes, and the majority of observed variation is effectively neutral. The predictions and implications of the neutral theory have proven immensely useful in this context, with applications spanning understanding within-host population structure, tracing the origins and spread of viral pathogens, predicting evolutionary dynamics, and modeling the emergence of drug resistance. We highlight the multiple ways in which the neutral theory has had an impact, which has been accelerated in the age of high-throughput, high-resolution genomics.
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Affiliation(s)
- Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge,
United Kingdom
- The Alan Turing Institute, London, United Kingdom
| | - Brittany Rife Magalis
- Institute for Genomics and Evolutionary Medicine, Temple University,
Philadelphia, PA
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16
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Mbondji-wonje C, Dong M, Wang X, Zhao J, Ragupathy V, Sanchez AM, Denny TN, Hewlett I. Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains. PLoS One 2018; 13:e0195661. [PMID: 29664930 PMCID: PMC5903597 DOI: 10.1371/journal.pone.0195661] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
Functional mapping of the 5’LTR has shown that the U3 and the R regions (U3R) contain a cluster of regulatory elements involved in the control of HIV-1 transcription and expression. As the HIV-1 genome is characterized by extensive variability, here we aimed to describe mutations in the U3R from various HIV-1 clades and CRFs in order to highlight strain specific differences that may impact the biological properties of diverse HIV-1 strains. To achieve our purpose, the U3R sequence of plasma derived virus belonging to different clades (A1, B, C, D, F2) and recombinants (CRF02_AG, CRF01_AE and CRF22_01A1) was obtained using Illumina technology. Overall, the R region was very well conserved among and across different strains, while in the U3 region the average inter-strains nucleotide dissimilarity was up to 25%. The TAR hairpin displayed a strain-distinctive cluster of mutations affecting the bulge and the loop, but mostly the stem. Like in previous studies we found a TATAA motif in U3 promoter region from the majority of HIV-1 strains and a TAAAA motif in CRF01_AE; but also in LTRs from CRF22_01A1 isolates. Although LTRs from CRF22_01A1 specimens were assigned CRF01_AE, they contained two NF-kB sites instead of the single TFBS described in CRF01_AE. Also, as previously describe in clade C isolates, we found no C/EBP binding site directly upstream of the enhancer region in CRF22_01A1 specimens. In our study, one-third of CRF02_AG LTRs displayed three NF-kB sites which have been mainly described in clade C isolates. Overall, the number, location and binding patterns of potential regulatory elements found along the U3R might be specific to some HIV-1 strains such as clade F2, CRF02_AG, CRF01_AE and CRF22_01A1. These features may be worth consideration as they may be involved in distinctive regulation of HIV-1 transcription and replication by different and diverse infecting strains.
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Affiliation(s)
- Christelle Mbondji-wonje
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- Department of Molecular Biology, Faculty of Medicine, Pharmacy and Biomedical sciences, University of Douala, Douala, Cameroon
- * E-mail: (CM); (IH)
| | - Ming Dong
- U.S. Military HIV Research Program, Silver Spring, Maryland United States of America
| | - Xue Wang
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jiangqin Zhao
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Viswanath Ragupathy
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Ana M. Sanchez
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States
| | - Thomas N. Denny
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States
| | - Indira Hewlett
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail: (CM); (IH)
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17
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Trends in Drug Resistance Prevalence, HIV-1 Variants and Clinical Status in HIV-1-infected Pediatric Population in Madrid: 1993 to 2015 Analysis. Pediatr Infect Dis J 2018; 37:e48-e57. [PMID: 28991889 DOI: 10.1097/inf.0000000000001760] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The expanded use of long-term antiretroviral treatments in infected children may exacerbate the problem of drug resistance mutations selection, which can compromise treatment efficiency. OBJECTIVE We describe the temporal trends of HIV drug resistance mutations and the HIV-1 variants during 23 years (1993 to March 2016) in the Madrid cohort of HIV-infected children and adolescents. METHODS We selected patients with at least one available HIV-1 pol sequence/genotypic resistance profile, establishing different groups according to the sampling year of first resistance data. We determined the prevalence of transmitted drug resistance mutations or acquired drug resistance mutations (DRM), the drug susceptibility among resistant viruses and HIV-1 variants characterized by phylogeny across time. RESULTS A total of 245 pediatric patients were selected, being mainly female, Spanish native, perinatally infected and carrying HIV-1 subtype B. At first sampling, most pediatric patients were on antiretroviral therapy and heavily pretreated. During 1993 to 2016, transmitted drug resistance mutations was found in 13 (26%) of 50 naive children [non-nucleoside reverse transcriptase inhibitors (NNRTI), 14.6%; nucleoside reverse transcriptase inhibitors (NRTI), 10.4%; protease inhibitors, 8.7%]. DRM appeared in 139 (73.2%) of 190 pretreated patients (NRTI, 64.5%; NNRTI, 36%; protease inhibitors, 35.1%). DRM to NNRTI was higher in last 5 years. Non-B variants infected 14.5% of children and adolescents of the Madrid Cohort, being mainly intersubtype recombinants (76.5%), including complex unique recombinant strains. They caused 3.4% infections before 2000, rising to 85.7% during 2011 to 2016. CONCLUSIONS Periodic surveillance resistance and molecular epidemiology studies in long-term pretreated HIV-infected pediatric populations are required to optimize treatment regimens. Results will permit a better understanding of long-time dynamics of viral resistance and HIV-1 variants in Spain.
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18
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Yebra G, Frampton D, Gallo Cassarino T, Raffle J, Hubb J, Ferns RB, Waters L, Tong CYW, Kozlakidis Z, Hayward A, Kellam P, Pillay D, Clark D, Nastouli E, Leigh Brown AJ. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project. PLoS One 2018; 13:e0192081. [PMID: 29389981 PMCID: PMC5794160 DOI: 10.1371/journal.pone.0192081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND & METHODS The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker. RESULTS The pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset. CONCLUSIONS The initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.
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Affiliation(s)
- Gonzalo Yebra
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Dan Frampton
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
| | | | - Jade Raffle
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
| | - Jonathan Hubb
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
| | - R. Bridget Ferns
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
- NIHR UCLH/UCL Biomedical Research Centre, London, United Kingdom
| | - Laura Waters
- Department of HIV Medicine, Mortimer Market Centre, Central & North West London NHS Trust, London, United Kingdom
| | - C. Y. William Tong
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
- Queen Mary University, London, United Kingdom
| | - Zisis Kozlakidis
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
- UCL Institute of Disease Informatics, Farr Institute of Health Informatics Research, London, United Kingdom
| | - Andrew Hayward
- UCL Institute of Epidemiology and Health Care, London, United Kingdom
| | - Paul Kellam
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Deenan Pillay
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
| | - Duncan Clark
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
- School of Life Sciences, University of Glasgow. Glasgow, United Kingdom
| | - Eleni Nastouli
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
- Department of Population, Policy and Practice, UCL GOS Institute of Child Health, London, United Kingdom
| | - Andrew J. Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
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19
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Prevalence and clinical impacts of HIV-1 intersubtype recombinants in Uganda revealed by near-full-genome population and deep sequencing approaches. AIDS 2017; 31:2345-2354. [PMID: 28832407 DOI: 10.1097/qad.0000000000001619] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVES HIV-1 subtypes A1 and D cocirculate in a rural community in Mbarara, Uganda. This study examines HIV-1 intersubtype recombination in this community under a full-genome sequencing context. We aim to estimate prevalence, examine time trends, and test for clinical correlates and outcomes associated with intersubtype recombinants. METHODS Near-full-genome HIV-1 Sanger sequence data were collected from plasma samples of 504 treatment-naïve individuals, who then received protease inhibitor or nonnucleoside reverse transcriptase inhibitor-containing regimens and were monitored for up to 7.5 years. Subtypes were inferred by Los Alamos Recombinant Identification Program (RIP) 3.0 and compared with Sanger/REGA and MiSeq/RIP. 'Nonrecombinants' and 'recombinants' infections were compared in terms of pretherapy viral load, CD4 cell count, posttherapy time to virologic suppression, virologic rebound, first CD4 rise above baseline and sustained CD4 recovery. RESULTS Prevalence of intersubtype recombinants varied depending on the genomic region examined: gag (15%), prrt (11%), int (8%), vif (10%), vpr (2%), vpu (9%), GP120 (8%), GP41 (18%), and nef (4%). Of the 200 patients with near-full-genome data, prevalence of intersubtype recombination was 46%; the most frequently observed recombinant was A1-D (25%). Sanger/REGA and MiSeq/RIP yielded generally consistent results. Phylogenetic tree revealed most recombinants did not share common ancestors. No temporal trend was observed (all P > 0.1). Subsequent subtype switches were detected in 27 of 143 (19%) study participants with follow-up sequences. Nonrecombinant versus recombinants infections were not significantly different in any pre nor posttherapy clinical correlates examined (all P > 0.2). CONCLUSION Intersubtype recombination was highly prevalent (46%) in Uganda if the entire HIV genome was considered, but was neither associated with clinical correlates nor therapy outcomes.
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20
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Lin B, Sun X, Su S, Lv C, Zhang X, Lin L, Wang R, Fu J, Kang D. HIV drug resistance in HIV positive individuals under antiretroviral treatment in Shandong Province, China. PLoS One 2017; 12:e0181997. [PMID: 28750025 PMCID: PMC5531464 DOI: 10.1371/journal.pone.0181997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/11/2017] [Indexed: 01/20/2023] Open
Abstract
The efficacy of antiretroviral drugs is limited by the development of drug resistance. Therefore, it is important to examine HIV drug resistance following the nationwide implementation of drug resistance testing in China since 2009. We conducted drug resistance testing in patients who were already on or new to HIV antiretroviral therapy (ART) in Shandong Province, China, from 2011 to 2013, and grouped them based on the presence or absence of drug resistance to determine the effects of age, gender, ethnicity, marital status, educational level, route of transmission and treatment status on drug resistance. We then examined levels of drug resistance the following year. The drug resistance rates of HIV patients on ART in Shandong from 2011 to 2013 were 3.45% (21/608), 3.38% (31/916), and 4.29% (54/1259), per year, respectively. M184V was the most frequently found point mutation, conferring resistance to the nucleoside reverse transcriptase inhibitor, while Y181C, G190A, K103N and V179D/E/F were the most frequent point mutations conferring resistance to the non-nucleoside reverse transcriptase inhibitor. In addition, the protease inhibitor drug resistance mutations I54V and V82A were identified for the first time in Shandong Province. Primary resistance accounts for 20% of the impact factors for drug resistance. Furthermore, it was found that educational level and treatment regimen were high-risk factors for drug resistance in 2011 (P<0.05), while treatment regimen was a high risk factor for drug resistance in 2012 and 2013 (P<0.05). Among the 106 drug-resistant patients, 77 received immediate adjustment of treatment regimen following testing, and 69 (89.6%) showed a reduction in drug resistance the following year. HIV drug resistance has a low prevalence in Shandong Province. However, patients on second line ART regimens and those with low educational level need continuous monitoring. Active drug resistance testing can effectively prevent the development of drug resistance.
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Affiliation(s)
- Bin Lin
- Shandong Center for AIDS Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Xiaoguang Sun
- Shandong Center for AIDS Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Shengli Su
- Shandong Center for AIDS Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Cuixia Lv
- Shandong Center for AIDS Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Xiaofei Zhang
- Shandong Center for AIDS Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Lin Lin
- Shandong Center for AIDS Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Rui Wang
- Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Jihua Fu
- Shandong Center for AIDS Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Dianmin Kang
- Shandong Center for AIDS Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
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Gangcuangco LMA, Sawada I, Tsuchiya N, Do CD, Pham TTT, Rojanawiwat A, Alejandria M, Leyritana K, Yokomaku Y, Pathipvanich P, Ariyoshi K. Regional Differences in the Prevalence of Major Opportunistic Infections among Antiretroviral-Naïve Human Immunodeficiency Virus Patients in Japan, Northern Thailand, Northern Vietnam, and the Philippines. Am J Trop Med Hyg 2017; 97:49-56. [PMID: 28719295 PMCID: PMC5508895 DOI: 10.4269/ajtmh.16-0783] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/22/2017] [Indexed: 11/07/2022] Open
Abstract
To identify regional differences in the distribution of opportunistic infections (OIs) among human immunodeficiency virus (HIV)-infected patients in Asia, the medical records of antiretroviral therapy (ART)-naïve patients who attended the following tertiary hospitals from 2003 to 2011 were reviewed: Nagoya Medical Center (NMC, Nagoya, Japan), Lampang Hospital (LPH, Lampang, northern Thailand), Bach Mai Hospital (BMH, Hanoi, northern Vietnam), and Philippine General Hospital (PGH, Manila, Philippines). Logistic regression analyses were performed to identify associations between country of origin and risk of major OIs. In total, 1,505 patients were included: NMC, N = 365; LPH, N = 442; BMH, N = 384; and PGH, N = 314. The median age was 32 years, and 73.3% of all patients were male. The median CD4 count was 200 cells/μL. Most patients at NMC and PGH were men who have sex with men. Injection drug users were most common at BMH (35.7%). Mycobacterium tuberculosis (TB) was most common at PGH (N = 75) but was rare at NMC (N = 4). Pneumocystis pneumonia (PCP) prevalence was highest at NMC (N = 74) and lowest at BMH (N = 13). Multivariable logistic regression showed increased odds of TB at PGH (adjusted odds ratio [aOR] = 42.2, 95% confidence interval [CI] = 14.6-122.1), BMH (aOR = 12.6, CI = 3.9-40.3), and LPH (aOR = 6.6, CI = 2.1-21.1) but decreased odds of PCP at BMH (aOR = 0.1, CI = 0.04-0.2) and LPH (aOR = 0.2, CI = 0.1-0.4) compared with those at NMC. The cryptococcosis risk was increased at LPH (aOR = 6.2, CI = 0.9-41.0) compared with that at NMC. Cytomegalovirus (CMV) retinitis prevalences were similar in all countries. OI prevalence remained high among ART-naïve patients in our cohort. The risks of TB, PCP, and cryptococcosis, but not CMV retinitis, differed between countries. Improved early HIV detection is warranted.
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Affiliation(s)
- Louie Mar A. Gangcuangco
- Institute of Tropical Medicine (NEKKEN), Graduate School of Biomedical Science, Nagasaki University, Nagasaki, Japan
- Bridgeport Hospital-Yale New Haven Health, Bridgeport, Connecticut
| | - Ikumi Sawada
- Institute of Tropical Medicine (NEKKEN), Graduate School of Biomedical Science, Nagasaki University, Nagasaki, Japan
| | - Naho Tsuchiya
- Institute of Tropical Medicine (NEKKEN), Graduate School of Biomedical Science, Nagasaki University, Nagasaki, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | | | | | | | - Marissa Alejandria
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | - Katerina Leyritana
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | | | | | - Koya Ariyoshi
- Institute of Tropical Medicine (NEKKEN), Graduate School of Biomedical Science, Nagasaki University, Nagasaki, Japan
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Chu M, Zhang W, Zhang X, Jiang W, Huan X, Meng X, Zhu B, Yang Y, Tao Y, Tian T, Lu Y, Jiang L, Zhang L, Zhuang X. HIV-1 CRF01_AE strain is associated with faster HIV/AIDS progression in Jiangsu Province, China. Sci Rep 2017; 7:1570. [PMID: 28484257 PMCID: PMC5431509 DOI: 10.1038/s41598-017-01858-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/03/2017] [Indexed: 11/21/2022] Open
Abstract
The goal of this study was to assess risk factors associated with HIV/AIDS progression. Between May 2007 and December 2014, 114 subjects were enrolled in Wuxi City and examined every 6 months. The pol gene sequence was amplified to ascertain the HIV-1 subtype. A Cox proportional hazards regression model was used to estimate the factors associated with HIV/AIDS progression. The median follow-up time for all 114 subjects was 26.70 months (IQR: 18.50-41.47), while the median progression time of the 38 progressed subjects was 24.80 months (IQR: 14.13-34.38). Overall, the CRF01_AE subtype was correlated with a significant risk of accelerated progression compared to non-CRF01_AE subtypes (HR = 3.14, 95%CI: 1.39-7.08, P = 0.006). In addition, a lower CD4 count (350-499) at baseline was associated with a risk of accelerated HIV/AIDS progression compared to higher CD4 count (≥500) (HR = 4.38, 95%CI: 1.95-9.82, P < 0.001). Furthermore, interaction analyses showed that HIV-1 subtypes interacted multiplicatively with transmission routes or CD4 count at baseline to contribute to HIV/AIDS progression (P = 0.023 and P < 0.001, respectively). In conclusion, the CRF01_AE subtype and a lower CD4 count at baseline tend to be associated with the faster progression of HIV/AIDS. Understanding the factors affecting HIV/AIDS progression is crucial for developing personalized management and clinical counselling strategies.
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Affiliation(s)
- Minjie Chu
- Department of Epidemiology and Biostatistics, School of Public Health, Nantong University, Nantong, Jiangsu, China
- School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia
| | - Wuhong Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Xuan Zhang
- Wuxi Municipal Centre for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Wenjie Jiang
- Department of Management Studies, University of Bath, Bath, UK
| | - Xiping Huan
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Xiaojun Meng
- Wuxi Municipal Centre for Disease Control and Prevention, Wuxi, Jiangsu, China
| | - Bowen Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yue Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yusha Tao
- Department of Epidemiology and Biostatistics, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Tian Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yihua Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Liying Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Lei Zhang
- School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, Australia
- Central Clinical School, Faculty of Medicine, Monash University, Melbourne, Australia
- Research Centre for Public Health, Tsinghua University, Beijing, China
| | - Xun Zhuang
- Department of Epidemiology and Biostatistics, School of Public Health, Nantong University, Nantong, Jiangsu, China.
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Rustanti L, Jin H, Lor M, Lin MH, Rawle DJ, Harrich D. A mutant Tat protein inhibits infection of human cells by strains from diverse HIV-1 subtypes. Virol J 2017; 14:52. [PMID: 28288662 PMCID: PMC5348743 DOI: 10.1186/s12985-017-0705-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background Nullbasic is a mutant HIV-1 Tat protein that inhibits HIV-1 replication via three independent mechanisms that disrupts 1) reverse transcription of the viral RNA genome into a DNA copy, 2) HIV-1 Rev protein function required for viral mRNA transport from the nucleus to the cytoplasm and 3) HIV-1 mRNA transcription by RNA Polymerase II. The Nullbasic protein is derived from the subtype B strain HIV-1BH10 and has only been tested against other HIV-1 subtype B strains. However, subtype B strains only account for ~10% of HIV-1 infections globally and HIV-1 Tat sequences vary between subtypes especially for subtype C, which is responsible for ~50% HIV-1 infection worldwide. These differences could influence the ability of Tat to interact with RNA and cellular proteins and thus could affect the antiviral activity of Nullbasic. Therefore, Nullbasic was tested against representative HIV-1 strains from subtypes C, D and A/D recombinant to determine if it can inhibit their replication. Methods Nullbasic was delivered to human cells using a self-inactivating (SIN) γ-retroviral system. We evaluated Nullbasic-mCherry (NB-mCh) fusion protein activity against the HIV-1 strains in TZM-bl cell lines for inhibition of transactivation and virus replication. We also examined antiviral activity of Nullbasic-ZsGreen1 (NB-ZSG1) fusion protein against the same strains in primary CD4+ T cells. The Nullbasic expression was monitored by western blot and flow cytometry. The effects of Nullbasic on primary CD4+ T cells cytotoxicity, proliferation and apoptosis were also examined. Results The results show that Nullbasic inhibits Tat-mediated transactivation and virus replication of all the HIV-1 strains tested in TZM-bl cells. Importantly, Nullbasic inhibits replication of the HIV-1 strains in primary CD4+ T cells without affecting cell proliferation, cytotoxicity or level of apoptotic cells. Conclusion A SIN-based γ-retroviral vector used to express Nullbasic fusion proteins improved protein expression particularly in primary CD4+ T cells. Nullbasic has antiviral activity against all strains from the subtypes tested although small differences in viral inhibition were observed. Further improvement of in γ-retroviral vector stable expression of Nullbasic expression may have utility in a future gene therapy approach applicable to genetically diverse HIV-1 strains. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0705-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lina Rustanti
- School of Medicine, the University of Queensland, Herston, QLD, 4029, Australia.,Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia.,National Institute of Health Research and Development, the Ministry of Health of Republic of Indonesia, Jalan Percetakan Negara 29, Central Jakarta, 10560, Indonesia
| | - Hongping Jin
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia
| | - Mary Lor
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia
| | - Min Hsuan Lin
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, 33302, Taiwan
| | - Daniel J Rawle
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia.,School of Chemistry and Molecular Biosciences, the University of Queensland, St. Lucia, QLD, 4072, Australia
| | - David Harrich
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia.
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Pagán I, Rojas P, Ramos JT, Holguín Á. Clinical Determinants of HIV-1B Between-Host Evolution and their Association with Drug Resistance in Pediatric Patients. PLoS One 2016; 11:e0167383. [PMID: 27907076 PMCID: PMC5132210 DOI: 10.1371/journal.pone.0167383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/14/2016] [Indexed: 01/10/2023] Open
Abstract
Understanding the factors that modulate the evolution of virus populations is essential to design efficient control strategies. Mathematical models predict that factors affecting viral within-host evolution may also determine that at the between-host level. Although HIV-1 within-host evolution has been associated with clinical factors used to monitor AIDS progression, such as patient age, CD4 cells count, viral load, and antiretroviral experience, little is known about the role of these clinical factors in determining between-host HIV-1 evolution. Moreover, whether the relative importance of such factors in HIV-1 evolution vary in adult and children patients, in which the course of infection is different, has seldom been analysed. To address these questions, HIV-1 subtype B (HIV-1B) pol sequences of 163 infected children and 450 adults of Madrid, Spain, were used to estimate genetic diversity, rates of synonymous and non-synonymous mutations, selection pressures and frequency of drug-resistance mutations (DRMs). The role and relative importance of patient age, %CD4, CD4/mm3, viral load, and antiretroviral experience in HIV-1B evolution was analysed. In the pediatric HIV-1B population, three clinical factors were primary predictors of virus evolution: Higher HIV-1B genetic diversity was observed with increasing children age, decreasing CD4/mm3 and upon antiretroviral experience. This was mostly due to higher rates of non-synonymous mutations, which were associated with higher frequency of DRMs. Using this data, we have also constructed a simple multivariate model explaining between 55% and 66% of the variance in HIV-1B evolutionary parameters in pediatric populations. On the other hand, the analysed clinical factors had little effect in adult-infecting HIV-1B evolution. These findings highlight the different evolutionary dynamics of HIV-1B in children and adults, and contribute to understand the factors shaping HIV-1B evolution and the appearance of drug-resistance mutation in pediatric patients.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Patricia Rojas
- HIV-1 Molecular Epidemiology Laboratory, Microbiology Department, Hospital Ramón y Cajal-IRYCIS and CIBER-ESP, Madrid, Spain
| | - José Tomás Ramos
- Hospital Clínico San Carlos and Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology Department, Hospital Ramón y Cajal-IRYCIS and CIBER-ESP, Madrid, Spain
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25
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Saladini F, Vicenti I. Role of phenotypic investigation in the era of routine genotypic HIV-1 drug resistance testing. Future Virol 2016. [DOI: 10.2217/fvl-2016-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emergence of drug resistance can seriously compromise HIV type-1 therapy and decrease therapeutic options. Resistance testing is highly recommended to guide treatment decisions and drug activity can be accurately predicted in the clinical setting through genotypic assays. While phenotypic systems are not suitable for monitoring drug resistance in routine laboratory practice, genotyping can misclassify unusual or complex mutational patterns, particularly with recently approved antivirals. In addition, phenotypic assays remain fundamental for characterizing candidate antiretroviral compounds. This review aims to discuss how phenotypic assays contributed to and still play a role in understanding the mechanisms of resistance of both licensed and investigational HIV type-1 inhibitors.
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Affiliation(s)
- Francesco Saladini
- Department of Medical Biotechnologies, University of Siena Italy, Policlinico Le Scotte, Viale Bracci 16 53100 Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena Italy, Policlinico Le Scotte, Viale Bracci 16 53100 Siena, Italy
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Alvarez P, Fernández McPhee C, Prieto L, Martín L, Obiang J, Avedillo P, Vargas A, Rojo P, Benito A, Ramos JT, Holguín Á. HIV-1 Variants and Drug Resistance in Pregnant Women from Bata (Equatorial Guinea): 2012-2013. PLoS One 2016; 11:e0165333. [PMID: 27798676 PMCID: PMC5087953 DOI: 10.1371/journal.pone.0165333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/10/2016] [Indexed: 12/16/2022] Open
Abstract
Objectives This is the first study describing drug resistance mutations (DRM) and HIV-1 variants among infected pregnant women in Equatorial Guinea (GQ), a country with high (6.2%) and increasing HIV prevalence. Methods Dried blood spots (DBS) were collected from November 2012 to December 2013 from 69 HIV-1 infected women participating in a prevention of mother-to-child transmission program in the Hospital Regional of Bata and Primary Health Care Centre María Rafols, Bata, GQ. The transmitted (TDR) or acquired (ADR) antiretroviral drug resistance mutations at partial pol sequence among naive or antiretroviral therapy (ART)-exposed women were defined following WHO or IAS USA 2015 lists, respectively. HIV-1 variants were identified by phylogenetic analyses. Results A total of 38 of 69 HIV-1 specimens were successfully amplified and sequenced. Thirty (79%) belonged to ART-experienced women: 15 exposed to nucleoside reverse transcriptase inhibitors (NRTI) monotherapy, and 15 to combined ART (cART) as first regimen including two NRTI and one non-NRTI (NNRTI) or one protease inhibitor (PI). The TDR rate was only found for PI (3.4%). The ADR rate was 37.5% for NNRTI, 8.7% for NRTI and absent for PI or NRTI+NNRTI. HIV-1 group M non-B variants caused most (97.4%) infections, mainly (78.9%) recombinants: CRF02_AG (55.2%), CRF22_A101 (10.5%), subtype C (10.5%), unique recombinants (5.3%), and A3, D, F2, G, CRF06_cpx and CRF11_cpx (2.6% each). Conclusions The high rate of ADR to retrotranscriptase inhibitors (mainly to NNRTIs) observed among pretreated pregnant women reinforces the importance of systematic DRM monitoring in GQ to reduce HIV-1 resistance transmission and to optimize first and second-line ART regimens when DRM are present.
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Affiliation(s)
- Patricia Alvarez
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Universitario Ramón y Cajal, IRYCIS and CIBERESP, Madrid, Spain
| | | | - Luis Prieto
- Pediatrics Department, Hospital Universitario de Getafe, Madrid, Spain
| | - Leticia Martín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Universitario Ramón y Cajal, IRYCIS and CIBERESP, Madrid, Spain
| | - Jacinta Obiang
- Pediatrics Department, Hospital Regional de Bata, Ministerio de Sanidad y Bienestar Social, Bata, Equatorial Guinea
| | - Pedro Avedillo
- Centro Nacional de Medicina Tropical, Instituto de Salud Carlos III-Madrid, RICET, Madrid, Spain
| | - Antonio Vargas
- Centro Nacional de Medicina Tropical, Instituto de Salud Carlos III-Madrid, RICET, Madrid, Spain
| | - Pablo Rojo
- Pediatrics Department, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Agustín Benito
- Centro Nacional de Medicina Tropical, Instituto de Salud Carlos III-Madrid, RICET, Madrid, Spain
| | - José Tomás Ramos
- Pediatrics Department, Hospital Universitario Clínico San Carlos, Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Universitario Ramón y Cajal, IRYCIS and CIBERESP, Madrid, Spain
- * E-mail:
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Non-R5-tropic HIV-1 in subtype A1 and D infections were associated with lower pretherapy CD4+ cell count but not with PI/(N)NRTI therapy outcomes in Mbarara, Uganda. AIDS 2016; 30:1781-8. [PMID: 27124899 DOI: 10.1097/qad.0000000000001128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Previous studies suggest that infection with non-R5-tropic subtype B HIV-1, compared with R5, is associated with a more rapid decline in CD4 cell count, but does not affect PI/(N)NRTI therapy outcome. Here, we explored clinical correlates associated with viral tropism in subtype A1 and D infections. METHODS HIV-1 subtype A1 (n = 196) and D (n = 143) pretherapy plasma samples and up to 7.5 years of posttherapy virologic and CD4 data were collected from a cross-sectional cohort in Mbarara, Uganda. Tropism and subtype were inferred using env V3 (geno2pheno) and gp41 (RIP) Sanger sequences. For each subtype, R5 infection was compared with non-R5 in terms of: pretherapy viral load and CD4 cell count (Mann-Whitney tests), and therapy outcomes, including time to virologic suppression, postsuppression virologic rebound, CD4 decline and CD4 recovery (log-rank tests). RESULTS A 94% of all patients in this study achieved virologic suppression within median 3 months posttherapy. In both subtypes, non-R5 infection was associated with lower pretherapy CD4 cell count (non-R5 vs. R5; A: median 57 vs. 147 cells/μl P = 0.005; D: 80 vs. 128 cells/μl P = 0.006). Multivariable linear regression confirmed that tropism, not subtype nor the interaction between subtype and tropism, was a significant predictor of pretherapy CD4 cell count (P < 0.0001). None of pretherapy viral load, time to virologic suppression, virologic rebound, CD4 decline nor CD4 recovery was significantly different (all P > 0.09). CONCLUSION Regardless of HIV-1 subtype or tropism, the majority of patients in this Ugandan cohort responded to therapy, even though non-R5 infection was associated with lower pretherapy CD4 cell count.
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Seu L, Mulenga LB, Siwingwa M, Sikazwe I, Lambwe N, Guffey MB, Chi BH. Characterization of HIV drug resistance mutations among patients failing first-line antiretroviral therapy from a tertiary referral center in Lusaka, Zambia. J Med Virol 2015; 87:1149-57. [PMID: 25754408 DOI: 10.1002/jmv.24162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2015] [Indexed: 11/10/2022]
Abstract
In settings of resource constraint, an understanding of HIV drug resistance can guide antiretroviral therapy (ART) at switch to second-line therapy. To determine the prevalence of such HIV drug resistance mutations (HIV DRM), we used an in-house sequencing assay in the pol gene (protease and partial reverse transcriptase) in a cohort of patients suspected of failing a first-line regimen, which in Zambia comprises two nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) and one non-nucleoside reverse transcriptase inhibitor (NNRTI). Our analysis cohort (n = 68) was referred to the University Teaching Hospital in Lusaka from November 2009 to October 2012. Median duration on first-line ART to suspected treatment failure was 3.2 years (IQR 1.7-4.7 years). The majority of patients (95%) harbored HIV-1 subtype C virus. Analysis of reverse transcriptase revealed M184V (88%), K103N/S (32%), and Y181C/I/V (41%) DRMs, with the latter conferring reduced susceptibility to the salvage therapy candidates etravirine and rilpivirine. Three patients (5%) had major protease inhibitor (PI) resistance mutations: all three had the V82A mutation, and one patient (Clade J virus) had a concurrent M46I, Q58E, and L76V DRM. HIV-1 genotyping revealed major and minor DRMs as well as high levels of polymorphisms in subtype C isolates from patients failing first-line antiretroviral therapy. Closer monitoring of DRM mutations at first-line failure can inform clinicians about future options for salvage therapy.
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Affiliation(s)
- Lillian Seu
- School of Medicine, University of Alabama at Birmingham, Alabama; Centre for Infectious Disease Research Zambia, Lusaka, Zambia
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Huang SW, Wang SF, Lin YT, Yen CH, Lee CH, Wong WW, Tsai HC, Yang CJ, Hu BS, Lin YH, Wang CT, Wang JJ, Hu Z, Kuritzkes DR, Chen YH, Chen YMA. Patients infected with CRF07_BC have significantly lower viral loads than patients with HIV-1 subtype B: mechanism and impact on disease progression. PLoS One 2014; 9:e114441. [PMID: 25502811 PMCID: PMC4263662 DOI: 10.1371/journal.pone.0114441] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/07/2014] [Indexed: 11/21/2022] Open
Abstract
The circulating recombinant form (CRF) 07_BC is the most prevalent HIV-1 strain among injection drug users (IDUs) in Taiwan. It contains a 7 amino-acid deletion in its p6gag. We conducted a cohort study to compare viral loads and CD4 cell count changes between patients infected with subtype B and CRF07_BC and to elucidate its mechanism. Twenty-one patients infected with CRF07_BC and 59 patients with subtype B were selected from a cohort of 667 HIV-1/AIDS patients whom have been followed up for 3 years. Generalized estimated equation was used to analyze their clinical data and the results showed that patients infected with CRF07_BC had significantly lower viral loads (about 58,000 copies per ml less) than patients with subtype B infection (p = 0.002). The replicative capacity of nine CRF07_BC and four subtype B isolates were compared and the results showed that the former had significantly lower replicative capacity than the latter although all of them were CCR5- tropic and non-syncytium inducing viruses. An HIV-1-NL4-3 mutant virus which contains a 7 amino-acid deletion in p6gag (designated as 7d virus) was generated and its live cycle was investigated. The results showed that 7d virus had significantly lower replication capacity, poorer protease-mediated processing and viral proteins production. Electron microscopic examination of cells infected with wild-type or 7d virus demonstrated that the 7d virus had poorer and slower viral maturation processes: more viruses attached to the cell membrane and higher proportion of immature virions outside the cells. The interaction between p6gag and Alix protein was less efficient in cells infected with 7d virus. In conclusion, patients infected with CRF07_BC had significantly lower viral loads than patients infected with subtype B and it may due to the deletion of 7 amino acids which overlaps with Alix protein-binding domain of the p6gag.
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Affiliation(s)
- Szu-Wei Huang
- Center for Infectious Disease and Cancer Research (CICAR), Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Sheng-Fan Wang
- Center for Infectious Disease and Cancer Research (CICAR), Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yu-Ting Lin
- Center for Infectious Disease and Cancer Research (CICAR), Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Hung Yen
- Center for Infectious Disease and Cancer Research (CICAR), Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Hao Lee
- Center for Infectious Disease and Cancer Research (CICAR), Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Wing-Wai Wong
- Section of Infectious Diseases, Department of Internal Medicine, Taipei Veterans' General Hospital, Taipei, Taiwan
| | - Hung-Chin Tsai
- Section of Infectious Diseases, Department of Internal Medicine, Kaohsiung Veterans' General Hospital, Kaohsiung, Taiwan
| | - Chia-Jui Yang
- Section of Infectious Diseases, Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Bor-Shen Hu
- Section of Infectious Diseases, Department of Internal Medicine, Taipei City Hospital, Taipei, Taiwan
| | - Yu-Huei Lin
- Section of Infectious Diseases, Department of Internal Medicine, Taichung Veterans' General Hospital, Taichung, Taiwan
| | - Chin-Tien Wang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jaang-Jiun Wang
- Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Zixin Hu
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel R. Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yen-Hsu Chen
- School of Medicine, Graduate Institute of Medicine, Sepsis Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yi-Ming Arthur Chen
- Center for Infectious Disease and Cancer Research (CICAR), Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Microbiology, Institute of Medical Research and Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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30
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Impact of human immunodeficiency virus type-1 sequence diversity on antiretroviral therapy outcomes. Viruses 2014; 6:3855-72. [PMID: 25333465 PMCID: PMC4213566 DOI: 10.3390/v6103855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/09/2014] [Accepted: 10/13/2014] [Indexed: 12/04/2022] Open
Abstract
Worldwide circulating HIV-1 genomes show extensive variation represented by different subtypes, polymorphisms and drug-resistant strains. Reports on the impact of sequence variation on antiretroviral therapy (ART) outcomes are mixed. In this review, we summarize relevant published data from both resource-rich and resource-limited countries in the last 10 years on the impact of HIV-1 sequence diversity on treatment outcomes. The prevalence of transmission of drug resistant mutations (DRMs) varies considerably, ranging from 0% to 27% worldwide. Factors such as geographic location, access and availability to ART, duration since inception of treatment programs, quality of care, risk-taking behaviors, mode of transmission, and viral subtype all dictate the prevalence in a particular geographical region. Although HIV-1 subtype may not be a good predictor of treatment outcome, review of emerging evidence supports the fact that HIV-1 genome sequence-resulting from natural polymorphisms or drug-associated mutations-matters when it comes to treatment outcomes. Therefore, continued surveillance of drug resistant variants in both treatment-naïve and treatment-experienced populations is needed to reduce the transmission of DRMs and to optimize the efficacy of the current ART armamentarium.
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Do HIV-1 non-B subtypes differentially impact resistance mutations and clinical disease progression in treated populations? Evidence from a systematic review. J Int AIDS Soc 2014; 17:18944. [PMID: 24998532 PMCID: PMC4083185 DOI: 10.7448/ias.17.1.18944] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 04/04/2014] [Accepted: 04/15/2014] [Indexed: 12/31/2022] Open
Abstract
There are 31 million adults living with HIV-1 non-B subtypes globally, and about 10 million are on antiretroviral therapy (ART). Global evidence to guide clinical practice on ART response in HIV-1 non-B subtypes remains limited. We systematically searched 11 databases for the period 1996 to 2013 for evidence. Outcomes documented included time to development of AIDS and/or death, resistance mutations, opportunistic infections, and changes in CD4 cell counts and viral load. A lack of consistent reporting of all clinical end points precluded a meta-analysis. In sum, genetic diversity that precipitated differences in disease progression in ART-naïve populations was minimized in ART-experienced populations, although variability in resistance mutations persisted across non-B subtypes. To improve the quality of patient care in global settings, recording HIV genotypes at baseline and at virologic failure with targeted non-B subtype-based point-of-care resistance assays and timely phasing out of resistance-inducing ART regimens is recommended.
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Impaired natural killer cell responses are associated with loss of the highly activated NKG2A(+)CD57(+)CD56(dim) subset in HIV-1 subtype D infection in Uganda. AIDS 2014; 28:1273-8. [PMID: 24959961 PMCID: PMC4032214 DOI: 10.1097/qad.0000000000000286] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Objective: Of the predominant HIV-1 subtypes in Uganda, subtype D infection confers a worse prognosis. HIV-1 infection causes perturbations to natural killer (NK) cells, and yet these cells can exert immune pressure on the virus and influence clinical outcome. Here, we studied NK cell activation and function in Ugandans with chronic untreated HIV-1 subtype D infection in comparison to uninfected community matched controls. Methods: Cryopreserved peripheral blood mononuclear cells (PBMCs) from 42 HIV-infected individuals and 28 HIV-negative controls were analysed using eight-colour flow cytometry. NK cell surface expression of CD16, CD56, CD57, HLA-DR and NKG2A were used to investigate activation, maturation and differentiation status. NK cell function was evaluated by measuring interferon-gamma (IFNγ) production in response to K562 cells, or interleukin (IL)-12 and IL-18. Results: CD56dim NK cells from HIV-infected individuals produced less IFNγ in response to IL-12 and IL-18 than did CD56dim NK cells from uninfected controls. Infected individuals had lower levels of CD56dim NK cells coexpressing the differentiation markers NKG2A and CD57 than controls. In addition, their NKG2A+CD57+ CD56dim NK cells displayed elevated activation levels as assessed by HLA-DR expression. Cytokine-induced IFNγ production correlated directly with coexpression of CD57 and NKG2A on CD56dim NK cells. Conclusion: HIV-1 subtype D infection is associated with impaired NK cell responsiveness to cytokines, decline of the NKG2A+CD57+ CD56dim NK cell subset, as well as elevated activation in this subset. These alterations within the NK cell compartment may contribute to immunopathogenesis of HIV-1 subtype D infection in Ugandans.
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Chan PA, Reitsma MB, DeLong A, Boucek B, Nunn A, Salemi M, Kantor R. Phylogenetic and geospatial evaluation of HIV-1 subtype diversity at the largest HIV center in Rhode Island. INFECTION GENETICS AND EVOLUTION 2014; 28:358-66. [PMID: 24721515 DOI: 10.1016/j.meegid.2014.03.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/17/2014] [Accepted: 03/24/2014] [Indexed: 12/01/2022]
Abstract
Individuals infected with HIV-1 non-B subtypes are understudied in the United States. Their characterization may augment prevention and treatment interventions. We examined the regional molecular epidemiology of non-B subtypes using a combined phylogenetic and geospatial approach. HIV-1 pol sequences and clinical data obtained for routine clinical care were aggregated from 2004 to 2011 at the largest HIV center in Rhode Island. Subtyping was performed by neighbor-joining and maximum-likelihood phylogeny and compared across eight commonly used tools (HIVdb, REGA, RIP, NCBI, Geno2Pheno, EuResist, jpHMM and STAR) using proportional odds ordinal regression. Individuals with non-B subtypes were characterized according to demographics and risk factors for infection, intra-subtype clustering by maximum-likelihood phylogeny, and geospatial hotspot analysis using Getis-Ord Gi(∗) statistics. Of 1277 unique sequences, phylogenetic subtyping demonstrated 8.3% (N=106, 95% CI 6.8-10%) non-B subtypes and circulating recombinant forms (CRFs): CRF02_AG=46; A=15; C=15; CRF01_AE=6; CRF06_CPX=5; CRF14_BG=5; G=3; CRF43_02G=3; D=3; CRF24_BG=3; CRF11_CPX=1; F1=1. Compared to phylogeny, Geno2Pheno was the most concordant (86% exact match) followed by REGA (85%), EuResist (85%) and STAR (82%). Of 106 individuals with non-B subtypes, 50% were male, 71% acquired infection through heterosexual transmission; 76%, were born in Africa, 6% Southeast Asia, 5% the United States, 3% Central America, 1% Europe, and 9% unknown. Eighty percent of CRF02_AG, 93% of A and 87% of C sequences were from African-born individuals. Twenty-two percent of non-B subtypes formed transmission clusters, including a significant number of younger individuals with perinatally-acquired infection. Geospatial analyses revealed hotspots of B and non-B subtypes in the state capital with a more concentrated focus among non-B subtypes. Molecular examination of regional HIV diversity revealed a larger than expected non-subtype B infected population, mostly born in Africa, with low ongoing regional transmission. Phylogenetic and geospatial characterization of infection clusters is helpful to identify targets for treatment and prevention interventions.
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Affiliation(s)
- Philip A Chan
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA.
| | - Marissa B Reitsma
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Allison DeLong
- Center for Statistical Sciences, Brown University, Providence, RI, USA
| | | | - Amy Nunn
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Marco Salemi
- Department of Pathology, University of Florida, Gainesville, FL, USA
| | - Rami Kantor
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
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Sui H, Gui T, Jia L, Guo W, Han J, Liu Y, Bao Z, Li H, Li J, Li L. Different frequencies of drug resistance mutations among HIV-1 subtypes circulating in China: a comprehensive study. PLoS One 2014; 9:e91803. [PMID: 24663120 PMCID: PMC3963863 DOI: 10.1371/journal.pone.0091803] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/13/2014] [Indexed: 12/12/2022] Open
Abstract
The rapid spreading of HIV drug resistance is threatening the overall success of free HAART in China. Much work has been done on drug-resistant mutations, however, most of which were based on subtype B. Due to different genetic background, subtypes difference would have an effect on the development of drug-resistant mutations, which has already been proved by more and more studies. In China, the main epidemic subtypes are CRF07_BC, CRF08_BC, Thai B and CRF01_AE. The depiction of drug resistance mutations in those subtypes will be helpful for the selection of regimens for Chinese. In this study, the distributions difference of amino acids at sites related to HIV drug resistance were compared among subtype B, CRF01_AE, CRF07_BC and CRF08_BC strains prevalent in China. The amino acid composition of sequences belonging to different subtypes, which were obtained from untreated and treated individuals separately, were also compared. The amino acids proportions of 19 sites in RT among subtype B, CRF01_AE and CRF08_BC have significant difference in drug resistance groups (chi-square test, p<0.05). Genetic barriers analysis revealed that sites 69, 138, 181, 215 and 238 were significantly different among subtypes (Kruskal Wallis test, p<0.05). All subtypes shared three highest prevalent drug resistance sites 103, 181 and 184 in common. Many drug resistant sites in protease show surprising high proportions in almost all subtypes in drug-naïve patients. This is the first comprehensive study in China on different development of drug resistance among different subtypes. The detailed data will lay a foundation for HIV treatment regimens design and improve HIV therapy in China.
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Affiliation(s)
- Hongshuai Sui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Clinical Laboratory of Beidaihe 281 hospital, Qinhuangdao, Hebei province, China
| | - Tao Gui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Guo
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail: (JL); (LL)
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail: (JL); (LL)
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Abstract
Objective: HIV-1 is typically categorized by genetically distinct viral subtypes. Viral subtypes are usually compartmentalized by ethnicity and transmission group and, thus, convey important epidemiological information, as well as possibly influencing the rate of disease progression. We aim to describe the prevalence and time trends of subtypes observed among key populations living with HIV-1 in the UK. Design: Analyses of reverse transcriptase and protease sequences generated from HIV-1-positive antiretroviral-naive patients as part of routine resistance testing between 2002 and 2010 in all public health and NHS laboratories in the UK. Methods: Subtype was assigned centrally using the SCUEAL algorithm. Subtyping results were combined with data from the UK Collaborative HIV Cohort Study and the UK HIV and AIDS Reporting System. Analyses adjusted for the number of national HIV-1 diagnoses made each year within demographic subgroups. Viral subtypes were described overall, over time and by demographic subgroup. Results: Subtype B diagnoses (39.9%) have remained stable since 2005, whereas subtype C diagnoses (34.3%) were found to decline in prevalence from 2004. Across most demographic subgroups, the prevalence of non-B non-C subtypes has increased over time, in particular novel recombinant forms (9.9%), subtype G (2.7%), and CRF01 AE (2.0%). Conclusion: HIV-1 subtypes are increasingly represented across all demographic subgroups and this could be evidence of sexual mixing. Between 2002 and 2010, the prevalence of novel recombinant forms has increased in all demographic subgroups. This increasing genetic diversity and the effect of subtype on disease progression may impact future HIV-1 treatment and prevention.
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van der Kuyl AC, Bakker M, Jurriaans S, Back NKT, Pasternak AO, Cornelissen M, Berkhout B. Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013. Retrovirology 2013; 10:93. [PMID: 23985078 PMCID: PMC3765835 DOI: 10.1186/1742-4690-10-93] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/21/2013] [Indexed: 02/07/2023] Open
Abstract
An HIV-1 diagnostic laboratory was established in the Academic Medical Center (AMC) of the University of Amsterdam after the discovery of human immunodeficiency virus (HIV) as the cause of the acquired immunodeficiency syndrome (AIDS). The first AIDS patients were diagnosed here in 1981 and since 1983 we have tested the samples of 50992 patients using a variety of assays that greatly improved over the years. We will describe some of the basic results from this diagnostic laboratory and then focus on the spin-off in terms of the development of novel virus assays to detect super-infections and ultra-sensitive assays to measure the intracellular HIV-1 RNA load. We also review several original research findings in the field of HIV-1 virology that stem from initial observations made in the diagnostic unit. This includes the study of genetic defects in the HIV-1 genome and time trends of the replication fitness over 30 years of viral evolution, but also the description of novel HIV-1 variants in difficult-to-diagnose clinical specimen.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands.
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Ssemwanga D, Nsubuga RN, Mayanja BN, Lyagoba F, Magambo B, Yirrell D, Van der Paal L, Grosskurth H, Kaleebu P. Effect of HIV-1 subtypes on disease progression in rural Uganda: a prospective clinical cohort study. PLoS One 2013; 8:e71768. [PMID: 23951241 PMCID: PMC3741119 DOI: 10.1371/journal.pone.0071768] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 07/03/2013] [Indexed: 02/04/2023] Open
Abstract
Objective We examined the association of HIV-1 subtypes with disease progression based on three viral gene regions. Design A prospective HIV-1 clinical cohort study in rural Uganda. Methods Partial gag, env and pol genes were sequenced. Cox proportional hazard regression modelling was used to estimate adjusted hazard ratios (aHRs) of progression to: CD4≤250, AIDS onset and death, adjusted for sex, age and CD4 count at enrolment. Results Between 1990 and 2010, 292 incident cases were subtyped: 25% had subtype A, 45% had D, 26% had A/D recombinants, 1% had C and 4% were other recombinant forms. Of the 278 incident cases included in the disease progression analysis, 62% progressed to CD4≤250, 32% to AIDS, and 34% died with a higher proportion being among subtype D cases. The proportions of individuals progressing to the three endpoints were significantly higher among individuals infected with subtype D. Throughout the study period, individuals infected with subtype D progressed faster to CD4≤250, adjusted HR (aHR), (95% CI) = 1.72 (1.16–2.54), but this was mainly due to events in the period before antiretroviral therapy (ART) introduction, when individuals infected with subtype D significantly progressed faster to CD4≤250 than subtype A cases; aHR (95% CI) = 1.78 (1.01–3.14). Conclusions In this population, HIV-1 subtype D was the most prevalent and was associated with faster HIV-1 disease progression than subtype A. Further studies are needed to examine the effect of HIV-1 subtypes on disease progression in the ART period and their effect on the virological and immunological ART outcomes.
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Affiliation(s)
- Deogratius Ssemwanga
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Rebecca N. Nsubuga
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Billy N. Mayanja
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Frederick Lyagoba
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Brian Magambo
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Dave Yirrell
- Department of Medical Microbiology, Ninewells Hospital, Dundee, United Kingdom
| | | | - Heiner Grosskurth
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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Killian MS, Vyas GN, Mehta R, Young K, Ebrahim O. Possible transmission of human immunodeficiency virus-1 infection from an elite controller to a patient who progressed to acquired immunodeficiency syndrome: a case report. J Med Case Rep 2012; 6:291. [PMID: 22967353 PMCID: PMC3469400 DOI: 10.1186/1752-1947-6-291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 06/08/2012] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Most individuals infected with human immunodeficiency virus-1, in the absence of antiretroviral therapy, exhibit persistent virus replication and declining CD4+ cell numbers, and progress to acquired immunodeficiency syndrome within 10 years of infection. Elite controllers are rare individuals with human immunodeficiency virus-1 infection who can maintain undetectable plasma virus levels and remain asymptomatic without antiretroviral therapy. It has been proposed that elite controllers benefit from being infected with attenuated human immunodeficiency virus-1 variants. CASE PRESENTATION A 31-year-old African woman presented with human immunodeficiency virus-1 infection during pregnancy and was diagnosed with acquired immunodeficiency syndrome. Subsequently, her husband, a 31-year-old African man, was tested and found to be seropositive for human immunodeficiency virus-1. His plasma human immunodeficiency virus-1 ribonucleic acid level was found to be below the limit of detection of the clinical assay. CONCLUSION This report provides evidence for the first described case of human immunodeficiency virus-1 infection possibly transmitted from an elite controller to a patient who progressed to acquired immunodeficiency syndrome. This observation strengthens the case against avirulence as a mechanism that protects elite controllers.
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Affiliation(s)
- Michael Scott Killian
- Department of Medicine, University of California San Francisco, 513 Parnassus Avenue, Box 1270, San Francisco, CA, 94143, USA.
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